1. Field of the Invention
The invention provides nucleotide sequences which code for the dapF gene and a process for the fermentative preparation of L-lysine using coryneform bacteria in which the dapF gene is amplified.
2. Background Invention
L-Lysine is used in human medicine and in the pharmaceuticals industry, but in particular in animal nutrition.
It is known that L-lysine is prepared by fermentation of strains of coryneform bacteria, in particular Corynebacterium glutamicum. Because of its great importance, work is constantly being undertaken to improve the preparation process. Improvements to the process can relate to fermentation measures, such as for example stirring and supply of oxygen, or the composition of the nutrient media, such as for example the sugar concentration during the fermentation, or the working up to the product form by for example ion exchange chromatography, or the intrinsic output properties of the microorganism itself.
Methods of mutagenesis, selection and mutant selection are used to improve the output properties of these microorganisms. Strains which are resistant to antimetabolites, such for example the lysine analogue S-(2-aminoethyl)-cysteine, or are auxotrophic for amino acids of regulatory importance and produce L-lysine are obtained in this manner.
Methods using recombinant DNA techniques have also been employed for some years for improving Corynebacterium strains which produce L-lysine, by amplifying individual lysine biosynthesis genes and investigating the effect on the L-lysine production. Review articles in this context are to be found, inter alia, in Kinoshita (xe2x80x9cGlutamic Acid Bacteriaxe2x80x9d, in: Biology of Industrial Microorganisms, Demain and Solomon (Eds.), Benjamin Cummings, London, UK, 1985, 115-142), Hilliger (BioTec 2, 40-44 (1991)), Eggeling (Amino Acids 6:261-272 (1994)), Jetten and Sinskey (Critical Reviews in Biotechnology 15, 73-103 (1995)) and Sahm et al. (Annuals of the New York Academy of Science 782, 25-39 (1996)).
In prokaryotes, three different routes are known for the biosynthesis of D,L-diaminopimelate- or L-lysine. These routes differ in the reaction of L-piperidine-2,6-dicarboxylate (tetrahydrodipicolinate).
In the succinylase route, tetrahydrodipicolinate is converted into D,L diaminopimelate via a succinylation by tetrahydrodipicolinate succinylase, subsequent transamination (N-succinyl-amino-ketopimelate transaminase) of the keto group, desuccinylation (N-succinyl-amino-ketopimelate desuccinylase) and then epimerization (diaminopimelate epimerase) (Gilvarg, 1958, The Journal of Biological Chemistry, 233: 1501-1504).
In the acetylase route, which is present in Bacillus subtilis and Bacillus megaterium, the acylation of tetrahydrodipicolinate is carried out by an acetyl radical (Weinberger and Gilvarg, 1970, Journal of Bacteriology, 101:323-324).
A third biosynthesis route is described for B. sphaericus (Misono et al., 1976, Journal of Bacteriology, 137:22-27). In this biosynthesis step, which is called the dehydrogenase route, direct reductive amination of the tetrahydrodipicolinate to D,L-DAP takes place.
With the aid of genetic and enzymatic studies, Schrumpf et al. (Journal of Bacteriology 173, 4510-4516 (1991)) showed that in Corynebacterium glutamicum, lysine biosynthesis takes place both by the dehydrogenase route and by the succinylase route.
In vivo NMR studies by Marx et al., (Biotechnology and Bioengineering 56, 168-180 (1997)) and Sonntag (European Journal of Biochemistry 213: 1325-1331 (1993)) have shown that in Corynebacterium glutamicum both the succinylase route and the dehydrogenase route contribute towards the production of L-lysine.
The gene for desuccinylase (dapE) from Corynebacterium glutamicum has been cloned and sequenced by Wehrmannn et al. (Journal of Bacteriology 177: 5991-5993 (1995)). It has also be possible to clone and sequence the gene for succinylase (dapD) from Corynebacterium glutamicum (Wehrmannn et al,. Journal of Bacteriology 180, 3159-3165 (1998)).
The inventors had the object of providing new measures for improved fermentative preparation of L-lysine.
L-Lysine is used in human medicine, in the pharmaceuticals industry and in particular in animal nutrition. There is therefore a general interest in providing new improved processes for the preparation of L-lysine.
When L-lysine or lysine are mentioned in the following, not only the base but also the salts, such as for example lysine monohydrochloride or lysine sulfate, are also meant.
The invention provides an isolated polynucleotide from coryneform bacteria, comprising a polynucleotide sequence chosen from the group consisting of
a) polynucleotide which is identical to the extent of at least 70% to a polynucleotide which codes for a polypeptide which comprises the amino acid sequence of SEQ ID No. 2,
b) polynucleotide which is identical to the extent of at least 70% to a polynucleotide which codes for the polypeptide which is expressed by the dapF gene contained on plasmid pEC-XT99A-dapF in the deposited C. glutamicum strain DSM 12968,
c) polynucleotide which codes for a polypeptide which comprises an amino acid sequence which is identical to the extent of at least 70% to the amino acid sequence of SEQ ID No. 2,
d) polynucleotide which is complementary to the polynucleotides of a), b) or c), and
e) polynucleotide comprising at least 15 successive bases of the polynucleotide sequence of a), b), c) or d).
The invention also provides a polynucleotide preferably being a DNA which is capable of replication, comprising:
(i) the nucleotide sequence shown in SEQ ID no. 1, or
(ii) at least one sequence which corresponds to sequence (i) within the range of the degeneration of the genetic code, or
(iii) at least one sequence which hybridizes with the sequence complementary to sequence (i) or (ii), and optionally
(iv) sense mutations of neutral function in (i).
The invention also provides
a polynucleotide that is capable of replication in coryneform bacteria, which is preferably recombinant DNA, comprising the nucleotide sequence as shown in SEQ ID no. 1,
a polynucleotide that is capable of replication in coryneform bacteria, which is preferably recombinant DNA, which codes for a polypeptide which comprises the amino acid sequence as shown in SEQ ID No.2,
a vector containing the polynucleotide sequence as described in (i)-(iv) above, in particular pEC-XT99A-dapF, deposited as DSM 12968.
and coryneform bacteria serving as the host cell, which contain the vector a shuttle vector pEC-XT99A-dapF characterized at the restriction map shown in FIG. 2, which has been deposited under the designation DSM 12968.
The invention also provides polynucleotides which substantially comprise a polynucleotide sequence, which are obtainable by screening by means of hybridization of a corresponding gene library, which comprise the complete gene with the polynucleotide sequence corresponding to SEQ ID no. 1, with a probe which comprises the sequence of the polynucleotide mentioned, according to SEQ ID no. 1 or a fragment thereof, and isolation of the DNA sequence mentioned.
Polynucleotide sequences according to the invention are suitable as hybridization probes for RNA, CDNA and DNA, in order to isolate, full length cDNA which encodes diamindpimelate epimerase and to isolate those cDNA or genes which have a high similarity of sequence with that of the diaminopimelate epimerase gene.
Polynucleotide sequences according to the invention are furthermore suitable as primers for the preparation of DNA of genes which code for diaminopimelate epimerase by the polymerase chain reaction (PCR).
Such oligonucleotides which serve as probes or primers comprise at least 30, preferably at least 20, especially preferably at least 15 successive bases. Oligonucleotides which have a length of at least 40 or 50 base pairs are also suitable.
xe2x80x9cIsolatedxe2x80x9d means separated out of its natural environment.
xe2x80x9cPolynucleotidexe2x80x9d in general relates to polyribonucleotides and polydeoxyribonucleotides, it being possible for these to be non-modified RNA or DNA or modified RNA or DNA.
xe2x80x9cPolypeptidesxe2x80x9d is understood as meaning peptides or proteins which comprise two or more amino acids bonded via peptide bonds.
The polypeptides according to the invention include a polypeptide according to SEQ ID No. 2, in particular those with the biological activity of diaminopimelate epimerase, and also those which are identical to the extent of at least 70% to the polypeptide according to SEQ ID No. 2, and preferably are identical to the extent of 80% and in particular to the extent of 90% to 95% to the polypeptide according to SEQ ID no. 2, and have the activity mentioned.
The invention also provides a process for the fermentative preparation of L-lysine using coryneform bacteria which in particular already produce L-lysine, and in which the nucleotide sequences which code for the dapF gene are amplified, in particular over-expressed.
The term xe2x80x9camplificationxe2x80x9d in this connection describes the increase in the intracellular activity of one or more enzymes in a microorganism which are coded by the corresponding DNA, for example by increasing the number of copies of the gene or genes, using a potent promoter or using a gene which codes for a corresponding enzyme having a high activity, and optionally combining these measures.
The microorganisms which the present invention provides can prepare L-lysine from glucose, sucrose, lactose, fructose, maltose, molasses, starch, cellulose or from glycerol and ethanol. They can be representatives of coryneform bacteria, in particular of the genus Corynebacterium. Of the genus Corynebacterium, there may be mentioned in particular the species Corynebacterium glutamicum, which is known among specialists for its ability to produce L-amino acids.
Suitable strains of the genus Corynebacterium, in particular of the species Corynebacterium glutamicum, are, for example, the known wild-type strains
Corynebacterium glutamicum ATCC13032
Corynebacterium acetoglutamicum ATCC15806
Corynebacterium acetoacidophilum ATCC13870
Corynebacterium thermoaminogenes FERM BP-1539
Brevibacterium flavum ATCC14067
Brevibacterium lactofermentum ATCC13869 and
Brevibacterium divaricatum ATCC14020
and L-lysine-producing mutants or strains produced therefrom, such as, for example
Corynebacterium glutamicum FERM-P 1709
Brevibacterium flavum FERM-P 1708
Brevibacterium lactofermentum FERM-P 1712
Corynebacterium glutamicum FERM-P 6463 and (sic)
Corynebacterium glutamicum FERM-P 6464
Corynebacterium glutamicum DSM5715
The inventors have succeeded in isolating the new dapF gene of C. glutamicum which codes for the enzyme diaminopimelate epimerase (EC 5.1.1.7).
To isolate the dapF gene or also other genes of C. glutamicum, a gene library of this microorganism is first set up in E. coli. The setting up of gene libraries is described in generally known textbooks and handbooks. The textbook by Winnacker: Gene und Klone, Eine Einfxc3xchrung in die Gentechnologie (Verlag Chemie, Weinheim, Germany, 1990) or the handbook by Sambrook et al.: Molecular Cloning, A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1989) may be mentioned as an example. A well-known gene library is that of the E. coli K-12 strain W3110 set up in xcex vectors by Kohara et al. (Cell 50, 495-508 (1987)). Bathe et al. (Molecular and General Genetics, 252:255-265, 1996) describe a gene libray of C. glutamicum ATCC13032, which was set up with the aid of the cosmid vector SuperCos I (Wahl et al., 1987, Proceedings of the National Academy of Sciences USA, 84:2160-2164) in the E. coli K-12 strain NM554 (Raleigh et al., 1988, Nucleic Acids Research 16:1563-1575). Bxc3x6rmann et al. (Molecular Microbiology 6(3), 317-326)) in turn describe a gene library of C. glutamicum ATCC13032 using the cosmid pHC79 (Hohn and Collins, Gene 11, 291-298 (1980)). To prepare a gene library of C. glutamicum in E. coli it is also possible to use plasmids such as pBR322 (Bolivar, Life Sciences, 25, 807-818 (1979)) or pUC9 (Viera et al., 1982, Gene, 19:259-268). Suitable hosts are, in particular, those E. coli strains which are restriction- and recombination-defective. An example of these is the strain DH5xcex1mcr, which has been described by Grant et al. (Proceedings of the National Academy of Sciences USA, 87 (1990) 4645-4649). The long DNA fragments cloned with the aid of cosmids can then in turn be subcloned and subsequently sequenced in the usual vectors which are suitable for sequencing, such as is described for example by Sanger et al. (Proceedings of the National Academy of Sciences of the United States of America, 74:5463-5467, 1977).
The new DNA sequence of C. glutamicum which codes for the dapF gene and which is a constituent of the present invention as SEQ ID NO 1 was obtained in this manner. The amino acid sequence of the corresponding protein has furthermore been derived from the present DNA sequence by the methods described above. The resulting amino acid sequence of the dapF gene product is shown in SEQ ID NO 2.
Coding DNA sequences which result from SEQ ID NO 1 by the degeneracy of the genetic code are also a constituent of the invention. In the same way, DNA sequences which hybridize with SEQ ID NO 1 or parts of SEQ ID NO 1 are a constituent of the invention. Conservative amino acid exchanges, such as for example exchange of glycine for alanine or of aspartic acid for glutamic acid in proteins, are furthermore known among experts as xe2x80x9csense mutationsxe2x80x9d which do not lead to a fundamental change in the activity of the protein, i.e. are of neutral function. It is furthermore known that changes on the N and/or C terminus of a protein cannot substantially impair or can even stabilize the function thereof. Information in this context can be found by the expert, inter alia, in Ben-Bassat et al. (Journal of Bacteriology 169:751-757 (1987)), in O""Regan et al. (Gene 77:237-251 (1989)), in Sahin-Toth et al. (Protein Sciences 3:240-247 (1994)), in Hochuli et al. (Bio/Technology 6:1321-1325 (1988)) and in known textbooks of genetics and molecular biology. Amino acid sequences which result in a corresponding manner from SEQ ID NO 2 are also a constituent of the invention.
In the same way, DNA sequences which hybridize with SEQ ID NO 1 or parts of SEQ ID NO 1 are a constituent of the invention. Finally, DNA sequences which are prepared by the polymerase chain reaction (PCR) using primers which result from SEQ ID NO 1 are a constituent of the invention. Such oligonucleotides typically have a length of at least 15 base pairs.
Instructions for identifying DNA sequences by means of hybridization can be found by the expert, inter alia, in the handbook xe2x80x9cThe DIG System Users Guide for Filter Hybridizationxe2x80x9d from Boehringer Mannheim GmbH (Mannheim, Germany, 1993) and in Liebl et al. (International Journal of Systematic Bacteriology (1991) 41:255-260). Instructions for amplification of DNA sequences with the aid of the polymerase chain reaction (PCR) can be found by the expert, inter alia, in the handbook by Gait: Oligonukleotide [sic] synthesis: a practical approach (IRL Press, Oxford, UK, 1984) and in Newton and Graham: PCR (Spektrum Akademischer Verlag, Heidelberg, Germany, 1994).
The inventors have found that coryneform bacteria produce L-lysine in an improved manner after over-expression of the dapF gene.
To achieve an over-expression, the number of copies of the corresponding genes can be increased, or the promoter and regulation region or the ribosome binding site upstream of the structural gene can be mutated. Expression cassettes which are incorporated upstream of the structural gene act in the same way. By inducible promoters, it is additionally possible to increase the expression in the course of fermentative L-lysine production. The expression is likewise improved by measures to prolong the life of the m-RNA. Furthermore, the enzyme activity is also increased by preventing the degradation of the enzyme protein. The genes or gene constructions can either be present in plasmids with a varying number of copies, or can be integrated and amplified in the chromosome. Alternatively, an over-expression of the genes in question can furthermore be achieved by changing the composition of the media and the culture procedure.
Instructions in this context can be found by the expert, inter alia, in Martin et al. (Bio/Technology 5, 137-146 (1987)), in Guerrero et al. (Gene 138, 35-41 (1994)), Tsuchiya and Morinaga (Bio/Technology 6, 428-430 (1988)), in Eikmanns et al. (Gene 102, 93-98 (1991)), in European Patent Specification EPS 0 472 869, in U.S. Pat. No. 4,601,893, in Schwarzer and Pxc3xchler (Bio/Technology 9, 84-87 (1991), in Reinscheid et al. (Applied and Environmental Microbiology 60, 126-132 (1994)), in LaBarre et al. (Journal of Bacteriology 175, 1001-1007 (1993)), in Patent Application WO 96/15246, in Malumbres et al. (Gene 134, 15-24 (1993)), in Japanese Laid-Open Specification JP-A-10-229891, in Jensen and Hammer (Biotechnology and Bioengineering 58, 191-195 (1998)), in Makrides (Microbiological Reviews 60:512-538 (1996)) and in known textbooks of genetics and molecular biology.
An example of a plasmid with the aid of which the dapF gene can be over-expressed is pEC-XT99A-dapF (FIG. 2), which is contained in the strain DSM5715/pEC-XT99A-dapF. Plasmid pEC-XT99A-dapF is an E. coli-C. glutamicum shuttle vector based on the plasmid pEC-XT99A (FIG. 1). This plasmid vector contains the replication region of the plasmid pGA1 (U.S. Pat. No. 5,175,108) and the tetracycline resistance gene of the plasmid pAG1 (Accession No. AF121000 of the National Center for Biotechnology Information, Bethesda, Md., USA). Other plasmid vectors which are capable of replication in C. glutamicum, such as e.g. pEKEx1 (Eikmanns et al., Gene 102:93-98 (1991)) or pZ8-1 (EP-B 0 375 889) can be used in the same way.
In addition, it may be advantageous for the production of L-lysine to over-express one or more enzymes of the lysine biosynthesis route, in addition to the dapF gene. Thus, for example
at the same time the dapA gene which codes for dihydrodipicolinate synthase can be over-expressed (EP-B 0 197 335), or
at the same time a DNA fragment which imparts S-(2-aminoethyl)-cysteine resistance can be amplified (EP-A 0 088 166), or
at the same time the dapD gene which codes for tetradihydrodipicolinate succinylase (Wehrmann et al., Journal of Bacteriology 180, 3159-3165 (1998)), or
at the same time the dapE gene which codes for succinyldiaminopimelate desuccinylase (Wehrmann et al., Journal of Bacteriology 177:5991-5993 (1995)) can be over-expressed.
In addition to over-expression of the dapF gene it may furthermore be advantageous, for the production of L-lysine, to eliminate undesirable side reactions (Nakayama: xe2x80x9cBreeding of Amino Acid Producing Micro-organismsxe2x80x9d, in: Overproduction of Microbial Products, Krumphanzl, Sikyta, Vanek (eds.), Academic Press, London, UK, 1982).
The microorganisms prepared according to the invention can be cultured continuously or discontinuously in the batch process (batch culture) or in the fed batch (feed process) or repeated fed batch process (repetitive feed process) for the purpose of production of L-lysine. A summary of known culture methods is described in the textbook by Chmiel (Bioprozesstechnik 1. Einfxc3xchrung in die Bioverfahrenstechnik (Gustav Fischer Verlag, Stuttgart, 1991)) or in the textbook by Storhas (Bioreaktoren und periphere Einrichtungen (Vieweg Verlag, Braunschweig/Wiesbaden, 1994)).
The culture medium to be used must meet the requirements of the particular strains in a suitable manner. Descriptions of culture media for various microorganisms are contained in the handbook xe2x80x9cManual of Methods for General Bacteriologyxe2x80x9d of the American Society for Bacteriology (Washington D.C., USA, 1981). Sugars and carbohydrates, such as for example glucose, sucrose, lactose, fructose, maltose, molasses, starch and cellulose, oils and fats, such as for example soya oil, sunflower oil, groundnut oil and coconut fat, fatty acids, such as for example palmitic acid, stearic acid and linoleic acid, alcohols, such as for example glycerol and ethanol, and organic acids, such as for example acetic acid, can be used as the source of carbon. These substances can be used individually or as a mixture. Organic nitrogen-containing compounds, such as peptones, yeast extract, meat extract, malt extract, corn steep liquor, soya bean flour and urea, or inorganic compounds, such as ammonium sulphate, ammonium chloride, ammonium phosphate, ammonium carbonate and ammonium nitrate, can be used as the source of nitrogen. The sources of nitrogen can be used individually or as a mixture. Phosphoric acid, potassium dihydrogen phosphate or dipotassium hydrogen phosphate or the corresponding sodium-containing salts can be used as the source of phosphorus. The culture medium must furthermore comprise salts of metals, such as for example magnesium sulfate or iron sulfate, which are necessary for growth. Finally, essential growth substances, such as amino acids and vitamins, can be employed in addition to the abovementioned substances. Suitable precursors can moreover be added to the culture medium. The starting substances mentioned can be added to the culture in the form of a single batch, or can be fed in during the culture in a suitable manner.
Basic compounds, such as sodium hydroxide, potassium hydroxide, ammonia or aqueous ammonia, or acid compounds, such as phosphoric acid or sulfuric acid, can be employed in a suitable manner to control the pH. Antifoams, such as for example fatty acid polyglycol esters, can be employed to control the development of foam. Suitable substances having a selective action, for example antilbiotics, can be added to the medium to maintain the stability of plasmids. To maintain aerobic conditions, oxygen or oxygen-containing gas mixtures, such as for example air, are introduced into the culture. The temperature of the culture is usually 20xc2x0 C. to 45xc2x0 C., and preferably 25xc2x0 C. to 40xc2x0 C. Culturing is continued until a maximum of lysine has formed. This target is usually reached within 10 hours to 160 hours.
The analysis of L-lysine can be carried out by anion exchange chromatography with subsequent ninhydrin derivatization, as described by Spackman et al. (Analytical Chemistry, 30, (1958), 1190).
The following microorganisms have been deposited at the Deutsche Sammlung Fur Mikrorganismen und Zellkuturen (DSMZ=German Collection of Microorganisms and Cell Cultures, Mascheroder Web 1b, 38124 Braunschweig, Germany) in accordance with the Budapest Treaty: Corynebacterium glutamicum strain DSM5715/pEC-XT99A as DSM 12967; and Corynebacterium glutamicum strain DSM5715/pEC-XT99A-dapF as DSM 12968.
In particular, the deposit labeled accession number DSM 12968 refers to a sample of Corynebacterium glutamicum, containing plasmid pEC-XT99A-dapF, deposited under the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure. The deposit was made on Aug. 5, 1999 at the aforementioned international depository.
The process according to the invention is used for fermentative preparation of L-lysine.